Resolving marine and aquatic community diversity, species and population patterns with targeted metabarcoding assays: Examples from deep sea and coastal ecosystems

Background/Question/Methods Ecological sampling depends on accurate taxon identification, delineation, and abundances, yet is time consuming, expensive, involves considerable taxonomic expertise, and often is thwarted by lack of diagnostic morphological characters. Targeted metagenomic analyses entailing field sampling, high-throughput sequencing, and bioinformatics offer means to rapidly and accurately simultaneously characterize the species diversity and compositions of entire communities, including rare and cryptic taxa, along with their relative representation and population genetics.

Results/Conclusions

We present results of diagnostic high-throughput Illumina MiSeq assays developed to analyze communities of invertebrates and fishes for environmental (e)DNA water samples from the field, zooplankton net tows, and aquarium experiments. These analyses are especially useful for assessing species diversity responses of marine communities to changing conditions, including ocean acidification, temperature, and hypoxia. We also give examples of their use to discern population genetic variation, in context of temporal and special patterns. In our procedure, samples are quantified using synthetic internal standards for representative key taxa during PCR, and used to establish thresholds for potential error. Our custom bioinformatic pipeline assesses sequence read quality and output, and matches with database taxa reference sequences. Results from these metagenomic analyses demonstrate considerable application across marine ecosystems at a scale, accuracy, complexity, and capacity for automation not otherwise feasible.